Bigben2K: I dont know about you but I am not all that thrilled about draining a cooling system by running the pump dry. Probably will not hurt it but who knows, even for those types of pumps.
My recomendation:
Try tilting your case slightly so you can move your pump as much out of your case as possible and release the line going into your pump at the very bottom. That should get almost all the water out.
Either way, once you get your rig drained, put some kind of a valve at the lowest point of you system so you just have to put a hose on it and open the valve for draining. MUCH easier than what you are up against right now
Good luck though